Download fasta sequence files

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Matteo Ferla Matteo Ferla 3, 3 3 silver badges 16 16 bronze badges. Downloading a few sequences For this, you can use Entrez Direct as mentioned by dc BlueSky BlueSky 2 2 bronze badges. Whether you want a large number of files or just one file is, I guess, a personal choice. A multifasta file is fairly standard though.

I don't think you can create individual files for each sequence using epost and efetch ; you will have to either use a bash script or postprocess the efetch output using the unix tool split.

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Related 5. Hot Network Questions. If your system is stuck on an older version of Python, consider using a tool likeHomebrew or Linuxbrew to obtain a more up-to-dateversion. If you're on a reasonably fast connection, you might want to try running multiple downloads in parallel:. It is possible to download multiple formats by supplying a list of formats or simply download all formats:.

Note : The quotes are important. Again, this is a simple string match on the organismname provided by the NCBI. Then, pass the path to that file e.

You can make the string match fuzzy using the --fuzzy-genus option. This can be handy if you need to matcha value in the middle of the NCBI organism name, like so:. Note : The above command will download all bacterial genomes containing 'coelicolor' anywhere in theirorganism name from RefSeq. Note : The above command will download all RefSeq genomes belonging to Escherichia coli. Note : The above command will download the RefSeq genome belonging to Escherichia coli str.

K substr. It is also possible to download multiple species taxids or taxids by supplying the numbers in a comma-separated list:. In addition, you can put multiple species taxids or taxids into a file, one per lineand pass that filename to the --species-taxid or --taxid parameters, respectively. It is possible to also create a human-readable directory structure in parallel to mirroringthe layout used by NCBI:. This will use links to point to the appropriate files in the NCBI directory structure,so it saves file space.

Note that links are not supported on some Windows file systems and someolder versions of Windows. It is also possible to re-run a previous download with the --human-readable option. In this case, ncbi-genome-download will not download any new genome files, and just createhuman-readable directory structure. Note that if any files have been changed on the NCBI side,a file download will be triggered. If you want to filter for the 'relation to type material' column of theassembly summary file, you can use the --type-material option.

Multiple values can be given, separated by comma:. By default, ncbi-genome-download caches the assembly summary files for the respective taxonomicgroups for one day.

You can skip using the cache file by using the --no-cache option. The output of --help also shows the cache directory, should you want to remove any of the cachedfiles.

You can also use it as a method call.